Flagstat

flagstat

samtools-flagstat

Provides counts for each of 13 categories based primarily on bit flags in the FLAG field. Each category is broken up into QC pass or QC fail. For example the first row in the flagstat file will look like:

122 + 28 in total (QC-passed reads + QC-failed reads)

which means that of the total 150 reads 122 were marked as QC pass and 28 as QC fail. The other categories are in the same structure

Attribute	Description
n_reads	Total number of reads
secondary	?
supplementary	?
duplicates	Number of duplicate reads
mapped	Number of mapped reads
paired in sequencing	the read is paired in sequencing, no matter whether it is mapped in a pair
read1	counts read1
read2	counds read2
properly paired	reads mapped in a proper pair
with itself and mate pair mapped	number of reads where the read itself is mapped the mate is unmapped
singletons	number of reads where the read itself is unmapped the mate is mapped
with mate mapped to a different chr	number of reads with a mate mapped on a different chromosome
with mate mapped to a different chr (mapQ>-5)	number of reads with a mate on a different chromosome having a quality greater than 5